# 4.3.7. ENCORE Ensemble Similarity Calculations — `MDAnalysis.analysis.encore`

Author:

  Matteo Tiberti, Wouter Boomsma, Tone Bengtsen

Year:

  2015-2017

Copyright:

  Lesser GNU Public License v2.1+

Maintainer:

  Matteo Tiberti <matteo.tiberti@gmail.com>, mtiberti on github

Added in version 0.16.0.

Deprecated since version 2.8.0: This module is deprecated in favour of the MDAKit mdaencore and will be removed in MDAnalysis 3.0.0.

The module contains implementations of similarity measures between protein ensembles described in [1]. The implementation and examples are described in [2].

The module includes facilities for handling ensembles and trajectories through the `Universe` class, performing clustering or dimensionality reduction of the ensemble space, estimating multivariate probability distributions from the input data, and more. ENCORE can be used to compare experimental and simulation-derived ensembles, as well as estimate the convergence of trajectories from time-dependent simulations.

ENCORE includes three different methods for calculations of similarity measures between ensembles implemented in individual functions:

- Harmonic Ensemble Similarity : `hes()`

- Clustering Ensemble Similarity : `ces()`

- Dimensional Reduction Ensemble Similarity : `dres()`

as well as two methods to evaluate the convergence of trajectories:

- Clustering based convergence evaluation : `ces_convergence()`

- Dimensionality-reduction based convergence evaluation : `dres_convergence()`

When using this module in published work please cite [2].

## 4.3.7.1. Modules

- 4.3.7.1.1. Ensemble Similarity Calculations — `MDAnalysis.analysis.encore.similarity`
- 4.3.7.1.2. Clustering
- 4.3.7.1.3. Dimensionality reduction
- 4.3.7.1.4. Distance Matrix calculation — `MDAnalysis.analysis.ensemble.confdistmatrix`
- 4.3.7.1.5. Covariance calculation — `encore.covariance`
- 4.3.7.1.6. bootstrap procedures — `MDAnalysis.analysis.ensemble.bootstrap`
- 4.3.7.1.7. Utility functions for ENCORE

## 4.3.7.2. References

[1]

Kresten Lindorff-Larsen and Jesper Ferkinghoff-Borg. Similarity measures for protein ensembles. PLOS ONE, 4(1):1–13, 01 2009. doi:10.1371/journal.pone.0004203.

[2] (1,2)

Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen. Encore: software for quantitative ensemble comparison. PLOS Computational Biology, 11(10):1–16, 10 2015. doi:10.1371/journal.pcbi.1004415.